(R)-(+)-2-{[(3-Methyl-4-nitro-pyridin-2-yl)meth-yl]sulfin-yl}-1H-benzimidazole.

The title compound, C(14)H(12)N(4)O(3)S, is an inter-mediate of Dexlansoprazole, a proton pump inhibitor (PPI) mainly developed for anti-ulcer activity. The absolute configuration of the title compound was determined as R. The crystal structure reveals that the mol-ecules form chains along the b axis through N-H⋯N and C-H⋯O hydrogen-bonded dimers. These chains are connected via weak C-H⋯O hydrogen bonds.

Related literature

For the synthesis of the title compound, see: Kumar et al. (2009 ▶). For background to this class of anti-ulcer drugs, see: Arimori et al. (1998 ▶); Masa et al. (2001 ▶). For a related structure, see: Fujishima et al. (2002 ▶).

Experimental

Crystal data

C14H12N4O3S

M = 316.33

Monoclinic,

a = 7.7422 (13) Å

b = 11.0505 (15) Å

c = 8.2318 (13) Å

β = 103.697 (7)°

V = 684.24 (18) Å3

Z = 2

Mo Kα radiation

μ = 0.26 mm−1

T = 298 K

0.22 × 0.20 × 0.18 mm

Data collection

Rigaku Mercury diffractometer

Absorption correction: multi-scan (REQAB; Jacobson, 1998 ▶) T min = 0.942, T max = 0.950

7636 measured reflections

2752 independent reflections

2601 reflections with F 2 > 2σ(F 2)

R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.037

wR(F 2) = 0.038

S = 1.25

2752 reflections

215 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.48 e Å−3

Δρmin = −0.37 e Å−3

Absolute structure: Flack (1983 ▶), with 1292 Friedel pairs

Flack parameter: −0.02 (4)

Data collection: CrystalClear (Rigaku, 2005 ▶); cell refinement: CrystalClear; data reduction: CrystalStructure (Molecular Structure Corporation & Rigaku, 2006 ▶); program(s) used to solve structure: SIR2004 (Burla et al. 2005 ▶); program(s) used to refine structure: CRYSTALS (Betteridge et al. 2003 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: CrystalStructure.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811029990/gw2104sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811029990/gw2104Isup3.hkl

Supplementary material file. DOI: 10.1107/S1600536811029990/gw2104Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C14H12N4O3S	F(000) = 328.00
Mr = 316.33	Dx = 1.535 Mg m−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71070 Å
Hall symbol: P 2yb	Cell parameters from 4183 reflections
a = 7.7422 (13) Å	θ = 1.8–27.5°
b = 11.0505 (15) Å	µ = 0.26 mm−1
c = 8.2318 (13) Å	T = 298 K
β = 103.697 (7)°	Prism, colourless
V = 684.24 (18) Å3	0.22 × 0.20 × 0.18 mm
Z = 2

Rigaku Mercury diffractometer	2601 reflections with F2 > 2σ(F2)
Detector resolution: 7.31 pixels mm-1	Rint = 0.025
ω scans	θmax = 27.5°
Absorption correction: multi-scan (REQAB; Jacobson, 1998)	h = −10→10
Tmin = 0.942, Tmax = 0.950	k = −13→13
7636 measured reflections	l = −7→10
2752 independent reflections

Refinement on F2	w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.037	(Δ/σ)max < 0.001
wR(F2) = 0.038	Δρmax = 0.48 e Å−3
S = 1.25	Δρmin = −0.37 e Å−3
2752 reflections	Absolute structure: Flack (1983), with 1292 Friedel pairs
215 parameters	Flack parameter: −0.02 (4)
H atoms treated by a mixture of independent and constrained refinement

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt).

	x	y	z	Uiso*/Ueq
S1	0.23549 (4)	0.46611 (4)	0.34638 (4)	0.0355 (1)
O1	0.24188 (14)	0.57292 (10)	0.23887 (14)	0.0447 (3)
O2	−0.55199 (16)	0.35772 (11)	0.11414 (16)	0.0604 (4)
O3	−0.57873 (16)	0.49507 (15)	−0.07757 (16)	0.0692 (5)
N1	0.51652 (18)	0.57978 (12)	0.55851 (18)	0.0374 (4)
N2	0.52568 (17)	0.37538 (12)	0.56996 (17)	0.0364 (4)
N3	−0.10635 (16)	0.66905 (11)	0.35720 (17)	0.0430 (4)
N4	−0.50763 (15)	0.45265 (15)	0.05912 (16)	0.0469 (4)
C1	0.43749 (15)	0.47231 (17)	0.50384 (15)	0.0352 (3)
C2	0.8180 (2)	0.36409 (15)	0.7887 (2)	0.0410 (5)
C3	0.9495 (2)	0.43573 (13)	0.8856 (2)	0.0438 (5)
C4	0.9417 (2)	0.56196 (15)	0.8789 (2)	0.0461 (5)
C5	0.8050 (2)	0.62249 (14)	0.7738 (2)	0.0417 (5)
C6	0.6711 (2)	0.55050 (13)	0.67435 (19)	0.0343 (5)
C7	0.6765 (2)	0.42432 (13)	0.6819 (2)	0.0336 (4)
C8	0.08069 (19)	0.50405 (15)	0.47829 (19)	0.0446 (5)
C9	−0.09062 (19)	0.54887 (13)	0.36425 (19)	0.0371 (4)
C10	−0.21640 (16)	0.46761 (16)	0.27169 (16)	0.0369 (3)
C11	−0.36204 (19)	0.52325 (14)	0.1662 (2)	0.0383 (4)
C12	−0.3806 (2)	0.64707 (13)	0.1538 (2)	0.0434 (5)
C13	−0.2491 (2)	0.71654 (15)	0.2537 (2)	0.0454 (5)
C14	−0.1877 (2)	0.33262 (15)	0.2842 (2)	0.0542 (6)
H1	0.494 (2)	0.6529 (16)	0.516 (2)	0.055 (5)*
H2	0.82390	0.27830	0.79360	0.0480*
H3	1.04750	0.39780	0.95950	0.0500*
H4	1.03430	0.60730	0.94910	0.0530*
H5	0.80050	0.70840	0.76880	0.0490*
H12	−0.48000	0.68360	0.08020	0.0510*
H13	−0.26100	0.80210	0.24930	0.0540*
H81	0.05890	0.43470	0.53870	0.0520*
H82	0.13040	0.56640	0.55450	0.0530*
H141	−0.29960	0.29300	0.26470	0.0660*
H142	−0.12570	0.30650	0.20380	0.0660*
H143	−0.12000	0.31340	0.39320	0.0660*

	U11	U22	U33	U12	U13	U23
S1	0.0266 (1)	0.0382 (2)	0.0387 (2)	0.0014 (2)	0.0019 (1)	−0.0015 (2)
O1	0.0386 (5)	0.0509 (6)	0.0422 (6)	0.0037 (4)	0.0051 (4)	0.0085 (4)
O2	0.0521 (7)	0.0478 (7)	0.0793 (9)	−0.0140 (6)	0.0116 (6)	−0.0158 (6)
O3	0.0467 (6)	0.1104 (13)	0.0441 (6)	−0.0083 (7)	−0.0019 (5)	−0.0079 (7)
N1	0.0350 (7)	0.0330 (6)	0.0412 (7)	0.0040 (5)	0.0029 (6)	0.0029 (6)
N2	0.0302 (6)	0.0355 (6)	0.0401 (7)	−0.0010 (5)	0.0015 (5)	0.0009 (6)
N3	0.0369 (7)	0.0406 (7)	0.0516 (8)	−0.0051 (5)	0.0110 (6)	−0.0030 (5)
N4	0.0320 (6)	0.0581 (9)	0.0502 (7)	−0.0062 (7)	0.0088 (5)	−0.0179 (8)
C1	0.0258 (5)	0.0395 (7)	0.0381 (6)	−0.0008 (7)	0.0030 (4)	−0.0012 (8)
C2	0.0389 (8)	0.0372 (8)	0.0435 (8)	0.0058 (7)	0.0028 (7)	0.0037 (7)
C3	0.0322 (7)	0.0528 (10)	0.0399 (8)	0.0058 (6)	−0.0043 (6)	0.0029 (7)
C4	0.0360 (8)	0.0552 (9)	0.0414 (9)	−0.0054 (7)	−0.0019 (7)	−0.0057 (8)
C5	0.0401 (8)	0.0343 (7)	0.0480 (9)	−0.0037 (6)	0.0053 (7)	−0.0025 (7)
C6	0.0311 (8)	0.0373 (8)	0.0350 (8)	0.0025 (6)	0.0089 (6)	0.0032 (6)
C7	0.0226 (7)	0.0407 (8)	0.0355 (8)	−0.0005 (5)	0.0032 (6)	0.0015 (5)
C8	0.0312 (7)	0.0580 (10)	0.0420 (8)	0.0063 (6)	0.0038 (6)	0.0046 (6)
C9	0.0280 (7)	0.0433 (8)	0.0399 (8)	0.0042 (5)	0.0079 (6)	0.0028 (6)
C10	0.0304 (5)	0.0385 (6)	0.0433 (6)	0.0012 (8)	0.0116 (5)	0.0006 (9)
C11	0.0290 (7)	0.0430 (8)	0.0449 (8)	−0.0024 (5)	0.0126 (7)	−0.0055 (6)
C12	0.0366 (8)	0.0427 (8)	0.0490 (9)	0.0051 (6)	0.0066 (6)	0.0053 (7)
C13	0.0431 (9)	0.0355 (7)	0.0566 (9)	0.0007 (6)	0.0097 (7)	0.0000 (7)
C14	0.0431 (9)	0.0394 (8)	0.0812 (13)	0.0029 (7)	0.0172 (9)	0.0010 (8)

S1—O1	1.4831 (12)	C6—C7	1.396 (2)
S1—C1	1.7806 (13)	C8—C9	1.515 (2)
S1—C8	1.8460 (16)	C9—C10	1.409 (2)
O2—N4	1.224 (2)	C10—C11	1.393 (2)
O3—N4	1.2229 (19)	C10—C14	1.508 (2)
N1—C1	1.363 (2)	C11—C12	1.377 (2)
N1—C6	1.381 (2)	C12—C13	1.380 (2)
N2—C1	1.317 (2)	C2—H2	0.9500
N2—C7	1.413 (2)	C3—H3	0.9500
N3—C9	1.3336 (19)	C4—H4	0.9500
N3—C13	1.333 (2)	C5—H5	0.9500
N4—C11	1.478 (2)	C8—H81	0.9500
N1—H1	0.881 (17)	C8—H82	0.9500
C2—C3	1.384 (2)	C12—H12	0.9500
C2—C7	1.400 (2)	C13—H13	0.9500
C3—C4	1.397 (2)	C14—H141	0.9500
C4—C5	1.372 (2)	C14—H142	0.9500
C5—C6	1.406 (2)	C14—H143	0.9500
O1—S1—C1	104.84 (7)	C9—C10—C14	121.46 (13)
O1—S1—C8	106.76 (7)	N4—C11—C12	115.39 (14)
C1—S1—C8	98.26 (6)	N4—C11—C10	121.95 (14)
C1—N1—C6	105.78 (12)	C10—C11—C12	122.67 (15)
C1—N2—C7	103.05 (12)	C11—C12—C13	117.33 (15)
C9—N3—C13	118.24 (14)	N3—C13—C12	123.01 (15)
O2—N4—O3	124.37 (15)	C3—C2—H2	122.00
O2—N4—C11	118.23 (13)	C7—C2—H2	122.00
O3—N4—C11	117.38 (15)	C2—C3—H3	119.00
C1—N1—H1	129.6 (11)	C4—C3—H3	119.00
C6—N1—H1	123.1 (11)	C3—C4—H4	119.00
N1—C1—N2	115.09 (12)	C5—C4—H4	119.00
S1—C1—N1	121.48 (13)	C4—C5—H5	122.00
S1—C1—N2	123.35 (13)	C6—C5—H5	122.00
C3—C2—C7	116.71 (14)	S1—C8—H81	110.00
C2—C3—C4	121.98 (15)	S1—C8—H82	110.00
C3—C4—C5	122.11 (15)	C9—C8—H81	110.00
C4—C5—C6	116.34 (14)	C9—C8—H82	109.00
C5—C6—C7	121.95 (14)	H81—C8—H82	109.00
N1—C6—C5	131.98 (14)	C11—C12—H12	122.00
N1—C6—C7	106.07 (13)	C13—C12—H12	121.00
C2—C7—C6	120.90 (14)	N3—C13—H13	118.00
N2—C7—C6	110.00 (13)	C12—C13—H13	119.00
N2—C7—C2	129.10 (14)	C10—C14—H141	109.00
S1—C8—C9	107.75 (10)	C10—C14—H142	110.00
N3—C9—C8	114.20 (13)	C10—C14—H143	109.00
N3—C9—C10	124.54 (14)	H141—C14—H142	109.00
C8—C9—C10	121.22 (13)	H141—C14—H143	109.00
C9—C10—C11	114.19 (15)	H142—C14—H143	109.00
C11—C10—C14	124.31 (14)
O1—S1—C1—N1	31.07 (13)	C3—C2—C7—C6	0.4 (2)
O1—S1—C1—N2	−145.56 (12)	C2—C3—C4—C5	−1.2 (3)
C8—S1—C1—N1	−78.80 (12)	C3—C4—C5—C6	0.9 (2)
C8—S1—C1—N2	104.57 (12)	C4—C5—C6—N1	179.22 (16)
O1—S1—C8—C9	51.34 (12)	C4—C5—C6—C7	0.0 (2)
C1—S1—C8—C9	159.64 (11)	N1—C6—C7—N2	0.34 (18)
C6—N1—C1—S1	−177.91 (10)	N1—C6—C7—C2	179.94 (14)
C6—N1—C1—N2	−1.02 (17)	C5—C6—C7—N2	179.71 (14)
C1—N1—C6—C5	−178.93 (16)	C5—C6—C7—C2	−0.7 (2)
C1—N1—C6—C7	0.35 (17)	S1—C8—C9—N3	−99.34 (14)
C7—N2—C1—S1	178.01 (10)	S1—C8—C9—C10	78.74 (15)
C7—N2—C1—N1	1.18 (16)	N3—C9—C10—C11	1.2 (2)
C1—N2—C7—C2	179.54 (16)	N3—C9—C10—C14	178.94 (14)
C1—N2—C7—C6	−0.90 (17)	C8—C9—C10—C11	−176.73 (13)
C13—N3—C9—C8	176.84 (14)	C8—C9—C10—C14	1.1 (2)
C13—N3—C9—C10	−1.2 (2)	C9—C10—C11—N4	179.93 (14)
C9—N3—C13—C12	−0.1 (2)	C9—C10—C11—C12	0.1 (2)
O2—N4—C11—C10	36.3 (2)	C14—C10—C11—N4	2.2 (2)
O2—N4—C11—C12	−143.88 (15)	C14—C10—C11—C12	−177.62 (15)
O3—N4—C11—C10	−145.52 (15)	N4—C11—C12—C13	178.95 (14)
O3—N4—C11—C12	34.3 (2)	C10—C11—C12—C13	−1.2 (2)
C7—C2—C3—C4	0.5 (2)	C11—C12—C13—N3	1.2 (2)
C3—C2—C7—N2	179.93 (17)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N2i	0.881 (17)	2.553 (18)	3.425 (2)	170.5 (13)
C2—H2···O1ii	0.95	2.33	3.251 (2)	164.
C12—H12···O2iii	0.95	2.55	3.164 (2)	122.

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N2i	0.881 (17)	2.553 (18)	3.425 (2)	170.5 (13)
C2—H2⋯O1ii	0.95	2.33	3.251 (2)	164
C12—H12⋯O2iii	0.95	2.55	3.164 (2)	122

Symmetry codes: (i) ; (ii) ; (iii) .